I think I know where the amonia came from.

You really have been having a hard time with this. It will get better though. I think part of your problems are because you weren't starting from scratch. You have had to try to make things work with the set-up you already had. That is always more difficult.
I really do think that things are starting to come together. Give that rock some time to be nice and cured and you will be on your way.